Efficient Use of Bio-Inspired Nanofabrication in Soft Electronics

Self-assembly plays an important role in the formation of different nanostructures either organic or inorganic. Controlled assembly of molecules into higher ordered hierarchical structures on the other hand require a thorough insight into the interactive forces that lie behind such an assembly. The interface between organic and inorganic materials is thus of primary significance when it comes to the tasks of selective deposition and assembly of inorganic molecules through organic agents. One of the bacterial species that belong to the class α-proteobacteria called Magnetospirillum magneticum (classified as AMB-1) is investigated in this study and it is found that this species is able to fulfill the requirements that are imposed by the complexity of the selective deposition and controlled assembly tasks. AMB-1 contain single-domain crystals of magnetite (Fe3O4) called magnetosomes that sense the external magnetic field that is further utilized for cellular displacement (magnetotaxis) through lash-like cellular appendages called flagella. The two flagella located at the proximal and distal ends of the cell consists of a protein monomer flagellin. Individual flagellin in turn that are located on the periphery of each of the flagellum's central channel consists of four sub-domains, two inner domains (D0, D1) made up of alpha helices and two outer domains (D2, D3) made up of beta sheets. However, it is the domain D3 that is exposed to the surrounding micro-environment, thereby interacting with the components to be selectively deposited, in this case, carbon nanotubes (CNT). Based on the electromagnetic and molecular dynamics simulations and the real-time experimental analysis involving optical microscopy utilizing 50 micron diameter conductor (44AWG) magnetic coils as directional magnetic field generation centers to visualize the motion of free as well as loaded AMB-1 as well as electron microscopy (TEM & SEM) to analyze the interactive forces between CNT and AMB-1 flagellum, it is found that once the domain D3 is functionalized with either metallic (m-) or semiconducting (s-) carbon nanotubes (CNT), the AMB-1 cell can be used as an efficient carrier for selective deposition tasks. Two aspects that are of particular interest are the phenomenal control of direction exhibited by AMB-1 using locally generated magnetic field and the efficient interactive forces in the form of short range forces (van der Waals, hydrophobic interactions and hydrogen bonds) and long range forces (electrostatic interactions) between m-CNT or s-CNT and D3. Thus, it is recognized that a compound semiconductor manufacturing technology involving bacterial carriers and carbon-based materials such as carbon nanotubes would be a desirable choice in the future

Selective Manipulation of Nanoparticles in Very Large Scale Integration (VLSI) using Magnetotactic Bacteria

Magnetotactic bacteria are a group of prokaryotic cells that orient and migrate along the geomagnetic field lines for their physiological functions and anaerobic/microaerophilic requirements. We report the use of magnetotaxis i.e. sensitivity towadrs megnetic field of Magnetospirillum magneticum as a functional component in very large scale integration (VLSI) design and fabrication. It is known that magnetotaxis arises out of a chain of magnetic nanoparticles within the bacterial cell that acts as a dipole. We propose a simple MATLAB based analysis and modeling of magnetic field acting on the chain of nanoparticles around a current carrying microwire. COMSOL was used to design the appropriate solenoid mesh containing the microwires.Our simulation results show that it is possible to manipulate the bacteria as "skilled workers" to transport select nanoparticles conducive to microchip fabrication. The use of magnetotactic bacteria may lead to the design of biomolecule based transformative integrated circuits well below the current feature size

Image processing tool for the Microorganism cell counting and its recognition

Microorganism cell counting is a basic laboratory technique which was frequently used in Microbiology Lab, hospital and pharmaceutical company. The traditional technique which is called “Hemocytometer method” counts the cells smeared on Hemocytometer (A special micro slide) under a microscope. It is the most popular and cheapest way to count cells or microorganisms. However, Hemocytometer method is not always accurate enough and counting cells under microscopes is a tedious job. Therefore, the engineers have developed lots of new means to achieve higher accuracy and shorter processing times. But those new means require fastidious preparation and complicated operation. Furthermore, most basic labs cannot afford those equipments. Therefore, Hemocytometer method still is the top choice for most researchers. With my background and experience in computer science and biomedicine, I am developing simple software to improve the accuracy and reduce the counting time for Hemocytometer method. The general idea of this software is to digitally process the images taken under an optical microscope. The general steps are: Eliminating noise and impurities, Gridding recognition, Cell recognition, Cell counting and gathering the data. The benefit of this software is to achieve more accurate results while avoiding arduous tasks performed by the technicians and scientists

Residue Specific and Chirality Dependent Interactions between Carbon Nanotubes and Flagellin

Flagellum is a lash-like cellular appendage found in many single-celled living organisms. The flagellin protofilaments contain 11-helix dual turn structure in a single flagellum. Each flagellin consists of four sub-domains - two inner domains (D0, D1) and two outer domains (D2, D3). While inner domains predominantly consist of α-helices, the outer domains are primarily beta sheets with D3. In flagellum, the outermost sub-domain is the only one that is exposed to the native environment. This study focuses on the interactions of the residues of D3 of an R-type flagellin with 5nm long chiral (5,15) and arm-chair (12,12) single-walled carbon nanotubes (SWNT) using molecular dynamics simulation. It presents the interactive forces between the SWNT and the residues of D3 from the perspectives of size and chirality of the SWNT. It is found that the metallic (arm-chair) SWNT interacts the most with glycine and threonine residues through van der Waals and hydrophobic interactions, whereas the semiconducting (chiral) SWNT interacts largely with the area of protein devoid of glycine by van der Waals, hydrophobic interactions, and hydrogen bonding. This indicates a crucial role that glycine plays in distinguishing metallic from semiconducting SWNTs

Magnetotaxis as a Means for Nanofabrication

Magnetotactic bacteria (MTB), discovered in early 1970s contain single-domain crystals of magnetite (Fe3O4) called magnetosomes that tend to form a chain like structure from the proximal to the distal pole along the long axis of the cell. The ability of these bacteria to sense the magnetic field for displacement, also called magnetotaxis, arises from the magnetic dipole moment of this chain of magnetosomes. In aquatic habitats, these organisms sense the geomagnetic field and traverse the oxic-anoxic interface for optimal oxygen concentration along the field lines. Here we report an elegant use of MTB where magnetotaxis of Magnetospirillum magneticum (classified as AMB-1) could be utilized for controlled navigation over a semiconductor substrate for selective deposition. We examined 50mm long coils made out of 18AWG and 20AWG copper conductors having diameters of 5mm, 10mm and 20mm for magnetic field intensity and heat generation. Based on the COMSOL simulations and experimental data, it is recognized that a compound semiconductor manufacturing technology involving bacterial carriers and carbon-based materials such as graphene and carbon nanotubes would be a desirable choice in the future

Structural analysis of a trimeric assembly of the mitochondrial dynamin-like GTPase Mgm1.

The fusion of inner mitochondrial membranes requires dynamin-like GTPases, Mgm1 in yeast and OPA1 in mammals, but how they mediate membrane fusion is poorly understood. Here, we determined the crystal structure of Saccharomyces cerevisiae short Mgm1 (s-Mgm1) in complex with GDP. It revealed an N-terminal GTPase (G) domain followed by two helix bundles (HB1 and HB2) and a unique C-terminal lipid-interacting stalk (LIS). Dimers can form through antiparallel HB interactions. Head-to-tail trimers are built by intermolecular interactions between the G domain and HB2-LIS. Biochemical and in vivo analyses support the idea that the assembly interfaces observed here are native and critical for Mgm1 function. We also found that s-Mgm1 interacts with negatively charged lipids via both the G domain and LIS. Based on these observations, we propose that membrane targeting via the G domain and LIS facilitates the in cis assembly of Mgm1, potentially generating a highly curved membrane tip to allow inner membrane fusion

Crystal Structure of the C-Terminal Cytoplasmic Domain of Non-Structural Protein 4 from Mouse Hepatitis Virus A59

BACKGROUND:The replication of coronaviruses takes place on cytoplasmic double membrane vesicles (DMVs) originating in the endoplasmic reticulum (ER). Three trans-membrane non-structural proteins, nsp3, nsp4 and nsp6, are understood to be membrane anchors of the coronavirus replication complex. Nsp4 is localized to the ER membrane when expressed alone but is recruited into the replication complex in infected cells. It is revealed to contain four trans-membrane regions and its N- and C-termini are exposed to the cytosol. METHODOLOGY/PRINCIPAL FINDINGS:We have determined the crystal structures of the C-terminal hydrophilic domain of nsp4 (nsp4C) from MHV strain A59 and a C425S site-directed mutant. The highly conserved 89 amino acid region from T408 to Q496 is shown to possess a new fold. The wild-type (WT) structure features two monomers linked by a Cys425-Cys425 disulfide bond in one asymmetric unit. The monomers are arranged with their N- and C-termini in opposite orientations to form an "open" conformation. Mutation of Cys425 to Ser did not affect the monomer structure, although the mutant dimer adopts strikingly different conformations by crystal packing, with the cross-linked C-termini and parallel N-termini of two monomers forming a "closed" conformation. The WT nsp4C exists as a dimer in solution and can dissociate easily into monomers in a reducing environment. CONCLUSIONS/SIGNIFICANCE:As nsp4C is exposed in the reducing cytosol, the monomer of nsp4C should be physiological. This structure may serve as a basis for further functional studies of nsp4

Adjusting CA19-9 values with clinical stage and bilirubin to better predict survival of resectable pancreatic cancer patients: 5-year-follow-up of a single center

BackgroundPancreatic cancer mortality is growing every year, and radical resection is the most essential therapy strategy. It is critical to evaluate the long-term prognosis of individuals receiving radical surgery. CA19-9 is a biomarker for patient recurrence and survival, however obstructive jaundice has a significant impact on this index. Researchers have attempted to modify the index using various modification methods, but the results have been unsatisfactory. In this study, we adjusted CA19-9 values based on clinical stage and bilirubin and found that it provided better prediction than CA19-9 alone in assessing patients.MethodsWe analyzed over 5 years follow-up records of patients who underwent radical pancreatic cancer surgery between August 2009 and May 2017 in a single center. We investigated the association of risk factors with overall survival (OS) as well as disease-free survival (DFS) after surgery. Threshold values for high-risk features associated with poor prognosis in resectable pancreatic cancer were determined. The hazard ratios of the indicators were eventually examined under the stratification of patients’ clinical stages.ResultsA total of 202 patients were involved in the study. The optimum cut-off values for CA19-9 and CA19-9/TB for predicting overall survival were 219.4 (p = 0.0075) and 18.8 (p = 0.0353), respectively. CA19-9>219.4 increased the risk of patient mortality by 1.70 times (95% CI 1.217-2.377, p = 0.002), and tumor poor differentiation raised the risk by 1.66 times (95% CI 1.083-2.553, P = 0.02). Based on clinical stage stratification, we found discrepancies in the predictive efficacy of CA19-9 and CA19-9/TB. CA19-9 was a better predictor in clinical stage 1 (HR = 2.056[CI 95%1.169-3.616], P = 0.012), whereas CA19-9/TB indications were better in stages 2 (HR = 1.650[CI 95%1.023-2.662], P = 0.040) and 3 (HR = 3.989[CI95%1.145-13.896], P = 0.030).ConclusionsCA19-9, CEA, and tumor differentiation are predictors for patients with resectable PDAC. CA19-9 values can be adjusted based on clinical stage and bilirubin levels to better predict overall survival in patients with resectable PDAC. CA19-9>219.4 predicted poor survival in individuals in clinical stage 1, whereas CA19-9/TB>18.8 predicted poor survival for individuals in stages 2 and 3